It means rather than having the series in the bag going into Friday's third and final Test the Australians hold a 1-0 lead and Sri Lanka still have a chance to claim a share of the spoils with a win at the Sinhalese Sports Club.
But Clarke said his team's continued dominance over the hosts when they were on the field in Kandy bodes well for the final Test and he's confident of taking out the series in the island nation's capital.
'I think we can take a lot of positives out of this game,' Clarke said.
'Shaun (Marsh) making a hundred on debut. Michael Hussey scoring more runs. We've got Ricky Ponting coming back into the team, we're bowling really well and our fielding standards are pretty high.
'The boys should be full of confidence.
'Our goal has always been to win three Test matches here - unfortunately the rain has played a big part here. But our attitude will be the same come the third Test - we're there to win.
'Hopefully there's no rain - I've heard a whisper that it's raining in Colombo as we speak so hopefully that disappears.'
The first thing Clarke will want to confirm once the team arrives in Colombo on Tuesday is the fitness of fast bowler Ryan Harris.
The 31-year-old left the field for a period during Monday complaining of a stiff right hamstring and will undergo scans to determine the extent of any damage.
It means the spearhead, who has 11 wickets at 14.54 so far this series, could be in doubt if there's any problems with the muscle meaning Peter Siddle or James Pattinson could come into contention for the final Test.
'We're confident, if the scan shows nothing, that he'll certainly be available for the third Test,' Clarke said.
'If it does show something there's going to be a little bit of doubt.'